An analysis of the population genetics of restored Zostera marina plantings in Barnegat Bay, New Jersey

Within Barnegat Bay, New Jersey, eelgrass (Zostera marina) populations have declined by 62 % over the last 20 years. To better understand the consequences of this devastation, we have previously employed microsatellite DNA polymorphisms to analyze the population structure of Z. marina within Barnegat Bay, as well as along the eastern United States seaboard. We have restored populations of Z. marina in Barnegat Bay over the last 10 years to help assess the best planting conditions and ecotypes that might be used in long-term restoration strategies. In this study, we examined the genetic health of the restored populations compared to that of the donor eelgrass populations within the bay. Using microsatellites, we can identify which parental founding ecotypes survived the restoration process over multiple generations. The frequency of observed heterozygotes, although higher than in the natural populations, still indicates reduced levels of diversity and connectivity. The inbreeding frequency is high in the restored populations, but lower than what is seen in the native populations. All restored populations have effective population values >50, suggesting a high probability of survival in the short term.     

Zostera marina population genetics in Barnegat Bay, New Jersey, and implications for grass bed restoration

Within Barnegat Bay, New Jersey, Zostera marina populations have declined by 62% over the last 20 years, and restoration efforts have met with mixed success. We have completed a microsatellite-based genetic investigation of eight populations of Z. marina within Barnegat Bay to determine whether the genetic stock origins of the plants used in management projects may affect restoration success. Additionally, we assessed the genetic diversity of Z. marina in Barnegat Bay to better understand its population structure. Clonal diversity ranged from 0.70 to 0.95 for the populations studied. Individually, Barnegat Bay populations are not genetically diverse, and there is also little divergence among populations. The Atlantic populations had mean Hobs values (0.20–0.34) that were far lower than the Hexp values (0.69–0.83). Also, the F _IS values in all of the eastern populations indicate a surfeit of homozygotes over heterozygotes, suggesting a low degree of outcrossing in the Barnegat Bay populations. Six of the ten populations studied (Ham Island, Manahawkin Bay, Shelter Island, Marsh Elder, Harvey Cedar Sedge, and Long Island) show evidence of historical bottlenecks. Mean estimated F _ST values would suggest that most alleles are undergoing moderate genetic differentiation, with values that range from 0.06 to 0.13. Oyster Creek and Sedge Island demonstrate the largest estimated effective population sizes and may be the most appropriate populations for use in future eelgrass restoration projects.     

Encystment of the ciliate Boveria teredinidi in the tissues of the molluscan woodborer Bankia gouldi in Barnegat Bay,New Jersey

Histological sections of Bankia gouldi from several stations in Barnegat Bay, New Jersey, were found to contain encysted Boveria teredinidi. The process of encapsulation appeared to be of the leukocytic type, and there was usually considerable leukocytic infiltration into the tissues in the areas of the cysts. No cysts were observed in tissues of Teredo navalis, T. furcifera, or T. bartschi, although ciliates were observed on the gill surfaces of these species. This report is believed to be the first of encystment in B. gouldi.     

Application and assessment of a nutrient pollution indicator using eelgrass (Zostera marina L.) in Barnegat Bay-Little Egg Harbor estuary, New Jersey

Eutrophication degrades numerous estuaries worldwide and a myriad of assessment metrics have been developed. Here, we apply an example of a previously developed metric (Lee et al., 2004) designed to indicate incipient estuarine eutrophication to validate this technique in an already eutrophic estuary end-member, Barnegat Bay-Little Egg Harbor, New Jersey. The metric, termed ‘Nutrient Pollution Indicator’ (NPI) uses eelgrass (Zostera marina L.) as a bioindicator and is calculated as the ratio of leaf nitrogen content (%N) to area normalized leaf mass (mg dry wt cm⁻²). Eelgrass samples were collected along the entire length of the Barnegat Bay-Little Egg Harbor from June to October 2008 to determine if leaf chemistry and morphology reflect eutrophication status and a north-south gradient of nitrogen loading from the Barnegat Bay watershed. Nitrogen content, area normalized leaf mass, and NPI values all significantly (p < 0.05) varied temporally but not spatially. NPI values did not significantly correspond to the north-south gradient of nitrogen loading from the Barnegat Bay watershed. The NPI metric is therefore not deemed to reliably indicate estuarine eutrophic status. Differences between sampling effort (number of stations) and replication did not bias the overall conclusions.     

Development,metamorphosis, and natural history of the nudibranch Doridella obscura Verrill (Corambidae: Opisthobranchia)

The doridacean nudibranch Doridella obscura Verrill was raised through one complete generation in laboratory culture, and spawning behavior monitored for a year at monthly intervals in Barnegat Bay, New Jersey.The nudibranch deposited egg masses throughout the year in Barnegat Bay, and the larvae remained viable at temperatures ranging from 1.5 to 28 °C. At 25 °C the eggs hatch 4 days after oviposition, and the planktotrophic veliger larvae swim and feed for 9 days before they metamorphose. Settlement occurs specifically on the bryozoan Electro crustulenta (Pallas). The spirally coiled larval shell grows rapidly until the dorsal mantle fold is retracted from the aperture 5–6 days after hatching. Although starved larvae grow only slightly and do not metamorphose, they resume normal development on introduction of suitable food. Newly metamorphosed juveniles consume algae and debris on the surface of the bryozoan until they grow large enough to attack the living zooids of E. crustulenta.The life cycle of Doridella obscura is short (26 days at 25 °C), allowing the nudibranchs to take advantage of short-lived Electra crustulenta colonies in unstable habitats in bays and estuaries.     

Effects of Temperature and Salinity on Vibrio vulnificus Population Dynamics as Assessed by Quantitative PCR

The abundance of Vibrio vulnificus in coastal environments has been linked to water temperature, while its relationship to salinity is less clear. We have developed a culture-independent, most-probable-number quantitative PCR approach to examine V. vulnificus population dynamics in Barnegat Bay, N.J. Based on the combined analysis of our results from Barnegat Bay and from the literature, the present data show that (i) V. vulnificus population dynamics are strongly correlated to water temperature and (ii) although the general trend is for V. vulnificus abundance to be inversely correlated with salinity, this relationship depends on salinity levels. Irrespective of temperature, high abundances of V. vulnificus are observed at 5 to 10 ppt, which thus appears to be the optimal salinity regime for their survival. At 20 to 25 ppt, V. vulnificus abundances show a positive correlation to salinity. Unsuccessful attempts to resuscitate V. vulnificus, combined with our inability to detect cells during the winter despite an assay adapted to detect viable but nonculturable (VBNC) cells, suggest that the decline and eventual disappearance of V. vulnificus from the water column during the winter months is due primarily to a significant reduction in population size and is not only the consequence of cells entering the VBNC state. These findings are in line with the hypothesis that the sediment serves as a refuge for a subpopulation of V. vulnificus over the winter and weather-driven mixing events during the spring initiate a summer bloom in the water column.     

Comparison of Insect Gut Cellulase and Xylanase Activity Across Different Insect Species with Distinct Food Sources

Insect guts represent unique natural biocatalyst systems for biocatalyst discovery and biomass deconstruction mechanism studies. In order to guide the further research for enzyme discovery and biodiversity analysis, we carried out comprehensive xylanase and cellulase activity assays for the gut contents of three insect species representing different orders and food sources. The three insect species are grasshopper (Acrididae sp.), woodborer (Cerambycidae spp.), and silkworm (Bombyx mori) to represent the wood-consuming, grass-consuming, and leaf-consuming insects from Orthoptera, Coleoptera, and Lepidoptera orders, respectively. Generally speaking, the enzyme activity assays have shown that the cellulase and xylanase activities for grasshopper and woodborer guts are significantly higher than those of silkworm under various conditions. In addition, both pH and temperature have a significant impact on the enzyme activities in the gut contents. For the grasshopper gut, the means of xylanase and cellulase activities at pH 7 were 3,397 and 404 μM mg^?1 min^?1, which are significantly higher than the activities at pH 4 and 10 (P?<?0.05). However, woodborer guts have shown the highest cellulase activity at pH 10. The results suggested that systems similar to woodborer guts could be good resources for discovering alkaline-tolerant enzymes. Moreover, the enzyme activities in response to different substrate concentrations were also analyzed, which indicated that grasshopper gut had particularly high cellulase activity. The enzyme activities in response to the reaction time were also examined, and we found that the enzyme activities (micromolar per milligram per minute) of different insect gut juices in response to the increase of incubation time fit well to the power function equation (E _c = K ? t ^b ) with high coefficients (r ²?>?0.99). The newly developed model serves well to compare the characteristics of the enzyme mixtures among different insect species, which can be applied to other studies of natural biocatalyst systems for the future. Overall, the data indicated that grasshopper and woodborer guts are valuable resources for discovering the novel biocatalysts for various biorefinery applications.     

Trichomonas vaginalis Exosomes Deliver Cargo to Host Cells and Mediate Host∶Parasite Interactions

Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogential tract where it remains extracellular and adheres to epithelial cells. Infections range from asymptomatic to highly inflammatory, depending on the host and the parasite strain. Here, we use a combination of methodologies including cell fractionation, immunofluorescence and electron microscopy, RNA, proteomic and cytokine analyses and cell adherence assays to examine pathogenic properties of T. vaginalis. We have found that T.vaginalis produces and secretes microvesicles with physical and biochemical properties similar to mammalian exosomes. The parasite-derived exosomes are characterized by the presence of RNA and core, conserved exosomal proteins as well as parasite-specific proteins. We demonstrate that T. vaginalis exosomes fuse with and deliver their contents to host cells and modulate host cell immune responses. Moreover, exosomes from highly adherent parasite strains increase the adherence of poorly adherent parasites to vaginal and prostate epithelial cells. In contrast, exosomes from poorly adherent strains had no measurable effect on parasite adherence. Exosomes from parasite strains that preferentially bind prostate cells increased binding of parasites to these cells relative to vaginal cells. In addition to establishing that parasite exosomes act to modulate host∶parasite interactions, these studies are the first to reveal a potential role for exosomes in promoting parasite∶parasite communication and host cell colonization.     

Toxoplasma,testosterone, and behavior manipulation: the role of parasite strain,host variations,and intensity of infection

Toxoplasma gondii is an intracellular parasite involved in the etiology of various behavioral and hormonal alterations in humans and rodents. Various mechanisms, including induction changes of testosterone production, have been proposed in the etiology of behavioral alterations during T. gondii infection. However, controversy remains about the effects of T. gondii infection on testosterone production; in some studies, increased levels of testosterone were reported, whereas other studies reported decreased levels. This is a significant point, because testosterone has been shown to play important roles in various processes, from reproduction to fear and behavior. This contradiction seems to indicate that different factors--primarily parasite strains and host variations--have diverse effects on the intensity of T. gondii infection, which consequently has diverse effects on testosterone production and behavioral alterations. This paper reviews the role of parasite strains, host variations, and intensity of T. gondii infection on behavioral alterations and testosterone production, as well as the role of testosterone in the etiology of these alterations during toxoplasmosis.     

Nosema pyrausta infection in Macrocentrus grandii, a braconid parasite of the European corn borer, Ostrinia nubilalis

Macrocentrus grandii which develop within Nosema pyrausta-infected larvae of the European corn borer, Ostrinia nubilalis, develop direct systemic infections from the ingestion of spores at the time of larval emergence from the host. Infections adversely affect pupal development and adult longevity. Infected females are unable to transmit the microsporidian to additional corn borer hosts. Pathogen development in the parasite host appears identical to its development in the corn borer host and mature spores show no morphological differences in size or shape when observed at the ultrastructural level. The prevalence of infection in natural parasite populations is 53.8% and closely parallels the 56.7% prevalence of infection in corn borer populations. Results suggest N. pyrausta may play a significant role in limiting M. grandii populations when levels of N. pyrausta in corn borers are high.     

Assessing the potential benthic-pelagic coupling in episodic blue mussel (Mytilus edulis) settlement events within eelgrass (Zostera marina) communities

Coastal marine seagrass ecosystems are important nursery grounds for commercially and recreationally important species, and they serve as key settlement and recruitment sites for other species. We investigated several years (2001-2003) where episodic settlement events of blue mussels (Mytilus edulis) occurred in Barnegat Bay, NJ, USA. Population assessment indicated that blue mussels settled in eelgrass beds (Zostera marina) in late spring with peak densities exceeding 170,000 m⁻². Based on calculated filtration rates of M. edulis, we determined that for at least 53 days in 2001, the density and size distribution of M. edulis were sufficient to filter the water column volume in excess of twice a day, with maximum calculated filtration rates exceeding 8 m³ water m⁻² day⁻¹. While the settlement event in 2001 was very localized, in 2003, the settlement event was considerably more widespread throughout the bay, with maximum settling densities exceeding 175,000 individuals m⁻². Associated with these high densities, maximum calculated filtration rates exceeded 15 m³ water m⁻² day⁻¹. This filtration potential may have impeded the localized development of a brown-tide (Aureococcus anophagefferens) bloom in 2001, which occurred in other regions of the bay, but the widespread settlement event seen in 2003 may have impeded the development of any brown-tide blooms in Barnegat Bay during that summer. The decline in mussel densities throughout the summer may be a result of elevated water temperatures in this back bay, but at one site, the high settlement of M. edulis was followed by a substantial migration (>40 individuals m⁻²) of small sea stars (Asterias forbesii). In 2001, A. forbesii was a significant factor in reducing M. edulis density by the end of the summer at the Barnegat Inlet site and a community level assessment showed significant positive correlations between mussel aggregations and sea star densities (r=0.68-0.73, P<0.001). At this same site in 2003, the sea stars were again present in high densities (26 m⁻²) and were a potential mechanism for mussel decline. In other regions of the bay, sea star densities are very low, but numerous other predatory species exist, including blue crabs (Callinectes sapidus), green crabs (Carcinus maenus), spider crabs (Libinia spp.), and several Xanthid crabs. Given the high mussel densities seen in this study and the considerable predation by sea stars and other benthic predators, the benthic-pelagic coupling which these mussels provide in this system contributes to the high secondary production in these grass beds.     

Vertical transmission and pathological findings in the mother,the placenta and the offspring,during first and last thirds of gestation in a mouse model of congenital toxoplasmosis

We performed a study of congenital toxoplasmosis of the first and third gestation periods in mice, and determined its effects on the embryos/fetuses, the placentae and the maternal organs. We infected pregnant BALB/c mice by i.v. injection of 2.5‐–10.0 × 10⁶ tachyzoites of the ME49 T. gondii strain and euthanized them 72 h later. The tissues were analyzed by histopathology, immunohistochemistry and parasite-specific qPCR. Infections with the lowest dose induced remarkably different changes in the two thirds: a) all doses diminished the number of products/litter, the lowest dose only by 14%; but most embryos still visible were degenerated in the case of the first period, while the fetuses of the last third were perfectly preserved; b) the transmission rate in the first third was relatively high, but with a very low parasite burden; c) with the lowest dose, strong vascular changes (congestion, thrombosis and hemorrhage) predominated in the placentas of the first period, while they were absent in the last third; d) necrosis caused by T. gondii to maternal organs was much stronger during the last gestation period than in the first. Our results suggest that the vascular alterations at the placenta of the first third of pregnancy prevent embryo from large parasite burden, but provoke its death by starvation. In the last gestation period, there was poor control of parasite dissemination to the placenta and the fetus, but there was greater capacity of the product to defend itself from T. gondii.     

Chemical, histochemical, and histopathological studies on corals. Porites spp., parasitized by trematode metacercariae

The occurrence of the metacercaria of Plagioporus sp. encysted in two species of corals, Porites compressa and P. lobata, from Kaneohe Bay, Oahu, Hawaii, is reported. This parasite is covered with a bilayered metacercarial cyst the chemical compositions of which have been ascertained by histochemistry. Both of these cyst walls are believed to be secreted by the parasite. In addition, the cytochemical properties of the metacercaria and the adjacent host cells are reported.Histo- and cytopathological alterations in the epidermis and gastrodermis of the coral hosts were studied and such changes have been interpreted to have resulted from mechanical pressure exerted by the parasite.Because gross observations had revealed the presence of elevated nodules at the sites where the metacercariae occurred, chemical analysis was conducted to ascertain whether this larval trematode had induced hypercalcification in the hosts. However, calcium determinations of Decal in which pieces of parasitized coral tissue had been decalcified revealed that hypercalcification had not occurred.Examination of the cellular reactions in both species of Porites revealed that if the gastrodermis had been ruptured, partial encapsulation of the parasite occurs. The reaction cells include free cells of the mesoglea that become fused, accidentally trapped cnidoblasts and nutritive-muscular cells, and gastrodermal interstitial cells. Despite the partial encapsulation, the encysted metacercariae did not appear to be injured.     

Distribution,density, and habitat use among native and introduced populations of the Australasian burrowing isopod <Emphasis Type="Italic">Sphaeroma quoianum</Emphasis>

The Australasian burrowing isopod (Sphaeroma quoianum) has been introduced to numerous embayments along the Pacific coast of North America. In some bays, populations of S. quoianum can exceed tens of thousands of individuals m⁻³ and bioturbation by the isopods can exacerbate shoreline erosion. Within their native range, however, studies recognize S. quoianum primarily as a woodborer. We measured the distribution, prevalence, habitat use, density, and associated fauna of S. quoianum in two bays within the native range [Tamar estuary (Tamar), Tasmania and Port Phillip Bay (PPB), VIC, Australia] and in one bay where the isopods had been introduced (Coos Bay, OR, USA). Distribution, prevalence, and habitat use were determined from shoreline surveys. Densities and the associated fauna of S. quoianum were measured in three intertidal substrata (marsh bank, wood, and friable rock). In all embayments, S. quoianum occurred primarily between 5 and 30 salinity and 55−68% of sites harbored isopods. Habitat use varied between embayments. Distributional patterns suggest salinity is the primary factor that limits the establishment and spread of S. quoianum. Isopod densities in all substrata were greater in Coos Bay than in the Tamar or PPB, although only densities within marsh banks varied significantly. Similarities in the amount of habitat and food, and the burrow dwelling lifestyle of S. quoianum suggest habitat availability/quality, food levels, predation, and competition are not responsible for the large differences in density. Lack of parasites or disease in populations of S. quoianum introduced to Coos Bay could be responsible for the prolific densities observed.     

Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae,Rhodophyta) to Narragansett Bay,Rhode Island,USA

During ongoing DNA barcode (COI‐5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C. secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2‐3 spacer) to compare the Narragansett Bay C. secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C. secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.     

Aptamer Based,Non-PCR,Non-Serological Detection of Chagas Disease Biomarkers in Trypanosoma cruzi Infected Mice

Chagas disease affects about 5 million people across the world. The etiological agent, the intracellular parasite Trypanosoma cruzi (T. cruzi), can be diagnosed using microscopy, serology or PCR based assays. However, each of these methods has their limitations regarding sensitivity and specificity, and thus to complement these existing diagnostic methods, alternate assays need to be developed. It is well documented that several parasite proteins called T. cruzi Excreted Secreted Antigens (TESA), are released into the blood of an infected host. These circulating parasite antigens could thus be used as highly specific biomarkers of T. cruzi infection. In this study, we have demonstrated that, using a SELEx based approach, parasite specific ligands called aptamers, can be used to detect TESA in the plasma of T. cruzi infected mice. An Enzyme Linked Aptamer (ELA) assay, similar to ELISA, was developed using biotinylated aptamers to demonstrate that these RNA ligands could interact with parasite targets. Aptamer L44 (Apt-L44) showed significant and specific binding to TESA as well as T. cruzi trypomastigote extract and not to host proteins or proteins of Leishmania donovani, a related trypanosomatid parasite. Our result also demonstrated that the target of Apt-L44 is conserved in three different strains of T. cruzi. In mice infected with T. cruzi, Apt-L44 demonstrated a significantly higher level of binding compared to non-infected mice suggesting that it could detect a biomarker of T. cruzi infection. Additionally, Apt-L44 could detect these circulating biomarkers in both the acute phase, from 7 to 28 days post infection, and in the chronic phase, from 55 to 230 days post infection. Our results show that Apt-L44 could thus be used in a qualitative ELA assay to detect biomarkers of Chagas disease.     

A picornavirus-like pathogen of Cotylogaster occidentalis (Trematoda: Aspidogastrea), an intestinal parasite of freshwater mollusks

Nonoccluded, icosahedral picornavirus-like (PVL) particles, 23 nm in diameter, forming paracrystalline arrays were seen in the cytoplasm of various cells in Cotylogaster occidentalis. Viral inclusions were visible in live specimens and in sections prepared for light and electron microscopy. All worms examined over a 2-year period were found to be infected. Infections were naturally acquired and susceptibility was not associated with any particular developmental stages. Development of viral inclusions involved an increase in the inclusion volume, progressive accumulation and condensation of materials into the interior of the inclusions, and formation of multilamellar membrane networks. Virus particles were observed in the stroma of the inclusions in association with multilamellar spherical bodies. Mature PVL particles aggregated into polygonally shaped paracrystalline arrays. When such arrays occurred in the surface tegument, local disruption of the tegumentary membrane may liberate these particles into the environment. PVL particle production did not exhaust glycogen content of infected cells and did not appear to affect short-term survival of the parasite outside the molluscan host.     

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana,USA

We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.     

Higher parasite richness, abundance and impact in native versus introduced cichlid fishes

Empirical studies suggest that most exotic species have fewer parasite species in their introduced range relative to their native range. However, it is less clear how, ecologically, the loss of parasite species translates into a measurable advantage for invaders relative to native species in the new community. We compared parasitism at three levels (species richness, abundance and impact) for a pair of native and introduced cichlid fishes which compete for resources in the Panama Canal watershed. The introduced Nile tilapia, Oreochromis niloticus, was infected by a single parasite species from its native range, but shared eight native parasite species with the native Vieja maculicauda. Despite acquiring new parasites in its introduced range, O. niloticus had both lower parasite species richness and lower parasite abundance compared with its native competitor. There was also a significant negative association between parasite load (abundance per individual fish) and host condition for the native fish, but no such association for the invader. The effects of parasites on the native fish varied across sites and types of parasites, suggesting that release from parasites may benefit the invader, but that the magnitude of release may depend upon interactions between the host, parasites and the environment.     

Origin of the pork tapeworm Taenia solium in Bali and Papua,Indonesia

Global distributions of zoonotic pathogens have been strongly affected by the history of human dispersal and domestication of livestock. The pork tapeworm Taenia solium is distributed worldwide as the cause of neurocysticercosis, one of the most serious neglected tropical diseases. T. solium has been reported in Indonesia but only endemic to restricted areas such as Bali and Papua. Previous studies indicated the distinctiveness of a mitochondrial haplotype confirmed in Papua, but only one isolate has been examined to date. In this study, genetic characterization of T. solium and pigs in Bali and Papua was conducted to clarify the distributional history of the parasite. Mitochondrial haplotype network analysis clearly showed that Indonesian T. solium comprises a unique haplogroup which was the first to diverge among Asian genotypes, indicating its single origin and the fact that it was not introduced in the recent past from other area in Asia in which it is endemic. Although phylogenetic analysis based on the mitochondrial D-loop revealed multiple origins of pigs in Bali and Papua, the majority of pigs belonged to the Pacific Clade, which is widely dispersed throughout the Island Southeast Asia (ISEA) and Oceania due to Neolithic human dispersal. Given the results of our network analysis, it is likely that the Pacific Clade pigs played a key role in the dispersal of T. solium. The data suggest that T. solium was introduced from mainland Asia into Western Indonesia, including Bali, by modern humans in the late Pleistocene, or in the early to middle Holocene along with the Pacific Clade pigs. Introduction into New Guinea most likely occurred in the late Holocene through the spread of Pacific Clade pigs. Over time, T. solium has been eradicated from most of Indonesia through the middle to modern ages owing to religious and cultural practices.